Recent advances in genomics and proteomics made a vast number of nucleotide and peptide sequences available for analysis, and high-throughput screening of samples for the presence and/or quantity of numerous known genes or polypeptides has gained considerable interest in recent years. While all or almost all of the individual steps or processes in high-throughput screening are well known in the art, integration of such steps or processes into a single analytic device remains a challenge. Among other difficulties and depending on the particular detection method employed, handling requirements for fluid management (e.g., sample application, hybridization, stringency washing) and detection (e.g., electronic or optical detection) are often incompatible where a single platform is employed.
For example, where binding of an analyte is electronically detected, (e.g., Nanogen's Nanochip®) various steps, including capture probe loading, analyte binding, and washing of the chip are performed in one station (e.g., Nanochip® Loader), while binding analysis is performed in a separate detector station (e.g., Nanochip® Reader). Electronic detection often allows multiple reuse of a biochip, and typically exhibits significantly accelerated analyte binding. However, due to the separation of the fluidics station and the detection station, the operator must manually transfer the chip from one station to the other, requiring proper insertion and operator control to commence detection, which at least somewhat defies the concept of automated high-throughput analysis.
Similarly, where binding of an analyte is optically detected, various biochips are commercially available as arrays of capture probes disposed on a microscope glass slide. Detection of labeled analytes that are bound to the capture probes is then performed with a flatbed scanner that typically acquires fluorescence data from the array on the surface of the slide. High-throughput analysis of such arrays is often relatively inexpensive. However, various disadvantages remain. Among other things, true signals are frequently not acquired where the surface of the glass slide is uneven. Moreover, manual operation of such slides may result in inadvertent damage to the array. Still further, fluidics management (e.g., hybridization, washing, etc.) is generally performed in one or more devices that are separate from the detector, and therefore again require user manual intervention.
To circumvent at least some of the problems associated with arrays on a glass slide, binding of the analyte may be optically detected in a chip that is disposed in a housing (e.g., Genechip by Affymetrix). A housing advantageously protects the biochip from inadvertent damage, and may further control flow of fluids (e.g., volume and/or flow control). However, such systems generally require processing the chip in a fluidics/hybridization station for binding and washing of an analyte that is bound to the capture probes, while analyte binding is detected in a separate detector. Again, an operator needs to manually insert the chip into the detector and select the suitable detection protocol prior to analysis. Furthermore, as is the case with the microscopy slide arrays, detection of the signal typically requires that fluids be completely removed from the chip to prevent quenching of the signal or other undesirable optical effects.
In another approach for high-throughput screening, multi-well plates may be used in a robotic station that automatically transfers a multi-well plate from a fluidics station to a plate reader station (see e.g., robotic stations from Beckman, Hudson, Hamilton, Gilson, Perkin Elmer, or Quiagen). Such robotic stations often integrate fluidics and detection, and employ relatively inexpensive multi-well plates. Moreover, customization of multi-well plates is generally relatively simple and can often be done using the same robotic station. However, robotic stations for multi-well plates generally have a relatively large footprint, especially where several thousand samples per day are processed. Smaller modular systems are also commercially available, however, typically fail to provide integrated sample analysis. Still further, detection of analytes in multi-well based systems is generally limited to microplate readers, which often provide limited accuracy and only perform well in assays where optical detection is not critically impaired by variations in focal depth.
Thus, although various systems for high-throughput screening are known in the art, numerous problems still remain. Therefore, there is still a need for an improved methods and systems for high-throughput screening.